It is unclear whether the Alliance had a central location of government, on either Qo'noS, Cardassia or elsewhere.

Bajor became a sovereign planet in the Alliance by the late 24th century, after the Alliance liberated Bajor from the Terran Empire. In the latter half of the 24th century, a Terran rebellion against the Alliance was created due to interference from individuals from the primary universe. (DS9: "Crossover")

In 2382, five ships from the Klingon-Cardassian Alliance were endowed with enhanced weapons, shields, and structural integrity by the mirror-Pah'Wraith, who were trapped within an ion storm, and who had decided to take a more active role in the struggle for power in the mirror-Alpha Quadrant. Oddly, their bestowing of enhanced ship-power didn't end with the Alliance, as they also enhanced the ISS Descent from the Terran Empire. Only months later was the Descent's abilities taken away as a show of complete political support for the Klingon-Cardassian Alliance. ("Rising Empire", "Darkened Soil")

In 2410, certain personnel from the previous Klingon-Cardassian Alliance, as well as supporters from the Terran Empire, numerous Romulans, the mirror Dominion, the mirror Borg Collective, and others used temporal technology to effectively save the mirror Iconians from Leeta's temporal attacks on them, secretly taking them elsewhere and forming the larger Klingon-Cardassian-Iconian Alliance, sending agents to destabilize other powers, acquire additional support from other factions, and in the end, overthrow the Terran Empire itself. It was evidently governed by a council of several Regents of the different member factions. Whether or not they have effectively become the Klingon-Cardassian Alliance's successor, if they are simply allied with the existing Alliance/Rebellion, or something else, is still largely unknown.